@article{12667, abstract = {Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals.}, author = {Li, Ling and Goodrich, Carl Peter and Yang, Haizhao and Phillips, Katherine R. and Jia, Zian and Chen, Hongshun and Wang, Lifeng and Zhong, Jinjin and Liu, Anhua and Lu, Jianfeng and Shuai, Jianwei and Brenner, Michael P. and Spaepen, Frans and Aizenberg, Joanna}, issn = {1091-6490}, journal = {PNAS}, number = {32}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals}}, doi = {10.1073/pnas.2107588118}, volume = {118}, year = {2021}, } @inproceedings{12767, abstract = {Several problems in planning and reactive synthesis can be reduced to the analysis of two-player quantitative graph games. Optimization is one form of analysis. We argue that in many cases it may be better to replace the optimization problem with the satisficing problem, where instead of searching for optimal solutions, the goal is to search for solutions that adhere to a given threshold bound. This work defines and investigates the satisficing problem on a two-player graph game with the discounted-sum cost model. We show that while the satisficing problem can be solved using numerical methods just like the optimization problem, this approach does not render compelling benefits over optimization. When the discount factor is, however, an integer, we present another approach to satisficing, which is purely based on automata methods. We show that this approach is algorithmically more performant – both theoretically and empirically – and demonstrates the broader applicability of satisficing over optimization.}, author = {Bansal, Suguman and Chatterjee, Krishnendu and Vardi, Moshe Y.}, booktitle = {27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783030720155}, issn = {1611-3349}, location = {Luxembourg City, Luxembourg}, pages = {20--37}, publisher = {Springer Nature}, title = {{On satisficing in quantitative games}}, doi = {10.1007/978-3-030-72016-2_2}, volume = {12651}, year = {2021}, } @inproceedings{12909, author = {Schlögl, Alois and Elefante, Stefano and Hornoiu, Andrei and Stadlbauer, Stephan}, booktitle = {ASHPC21 – Austrian-Slovenian HPC Meeting 2021}, isbn = {978-961-6980-77-7}, location = {Virtual}, pages = {5}, publisher = {University of Ljubljana}, title = {{Managing software on a heterogenous HPC cluster}}, doi = {10.3359/2021hpc}, year = {2021}, } @misc{12987, abstract = {Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.}, author = {Koch, Eva and Morales, Hernán E. and Larsson, Jenny and Westram, Anja M and Faria, Rui and Lemmon, Alan R. and Lemmon, E. Moriarty and Johannesson, Kerstin and Butlin, Roger K.}, publisher = {Dryad}, title = {{Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis}}, doi = {10.5061/DRYAD.ZGMSBCCB4}, year = {2021}, } @misc{13057, abstract = {This dataset comprises all data shown in the figures of the submitted article "Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction". Additional raw data are available from the corresponding author on reasonable request.}, author = {Peruzzo, Matilda and Hassani, Farid and Szep, Grisha and Trioni, Andrea and Redchenko, Elena and Zemlicka, Martin and Fink, Johannes M}, publisher = {Zenodo}, title = {{Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction}}, doi = {10.5281/ZENODO.5592103}, year = {2021}, } @misc{13058, abstract = {The zip file includes source data used in the main text of the manuscript "Theory of branching morphogenesis by local interactions and global guidance", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.}, author = {Ucar, Mehmet C}, publisher = {Zenodo}, title = {{Source data for the manuscript "Theory of branching morphogenesis by local interactions and global guidance"}}, doi = {10.5281/ZENODO.5257160}, year = {2021}, } @misc{13061, abstract = {Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.}, author = {Casillas Perez, Barbara E and Pull, Christopher and Naiser, Filip and Naderlinger, Elisabeth and Matas, Jiri and Cremer, Sylvia}, publisher = {Dryad}, title = {{Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies}}, doi = {10.5061/DRYAD.7PVMCVDTJ}, year = {2021}, } @misc{13062, abstract = {This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.}, author = {Szep, Eniko and Sachdeva, Himani and Barton, Nicholas H}, publisher = {Dryad}, title = {{Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model}}, doi = {10.5061/DRYAD.8GTHT76P1}, year = {2021}, } @misc{13063, abstract = {We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.}, author = {Robinson, Matthew Richard}, publisher = {Dryad}, title = {{Probabilistic inference of the genetic architecture of functional enrichment of complex traits}}, doi = {10.5061/dryad.sqv9s4n51}, year = {2021}, } @misc{13068, abstract = {Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids".}, author = {Randriamanantsoa, Samuel and Papargyriou, Aristeidis and Maurer, Carlo and Peschke, Katja and Schuster, Maximilian and Zecchin, Giulia and Steiger, Katja and Öllinger, Rupert and Saur, Dieter and Scheel, Christina and Rad, Roland and Hannezo, Edouard B and Reichert, Maximilian and Bausch, Andreas R.}, publisher = {Zenodo}, title = {{Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids}}, doi = {10.5281/ZENODO.5148117}, year = {2021}, } @misc{13069, abstract = {To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.}, author = {Chauve, Laetitia and Hodge, Francesca and Murdoch, Sharlene and Masoudzadeh, Fatemah and Mann, Harry-Jack and Lopez-Clavijo, Andrea and Okkenhaug, Hanneke and West, Greg and Sousa, Bebiana C. and Segonds-Pichon, Anne and Li, Cheryl and Wingett, Steven and Kienberger, Hermine and Kleigrewe, Karin and de Bono, Mario and Wakelam, Michael and Casanueva, Olivia}, publisher = {Zenodo}, title = {{Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans}}, doi = {10.5281/ZENODO.5519410}, year = {2021}, } @misc{13072, abstract = {CpGs and corresponding mean weights for DNAm-based prediction of cognitive abilities (6 traits)}, author = {McCartney, Daniel L and Hillary, Robert F and Conole, Eleanor LS and Trejo Banos, Daniel and Gadd, Danni A and Walker, Rosie M and Nangle, Cliff and Flaig, Robin and Campbell, Archie and Murray, Alison D and Munoz Maniega, Susana and del C Valdes-Hernandez, Maria and Harris, Mathew A and Bastin, Mark E and Wardlaw, Joanna M and Harris, Sarah E and Porteous, David J and Tucker-Drob, Elliot M and McIntosh, Andrew M and Evans, Kathryn L and Deary, Ian J and Cox, Simon R and Robinson, Matthew Richard and Marioni, Riccardo E}, publisher = {Zenodo}, title = {{Blood-based epigenome-wide analyses of cognitive abilities}}, doi = {10.5281/ZENODO.5794028}, year = {2021}, } @misc{13080, abstract = {Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org)) We upload a pdf with extended data sets, and the raw data for these extended datasets as well.}, author = {Puglia, Denise and Martinez, Esteban and Menard, Gerbold and Pöschl, Andreas and Gronin, Sergei and Gardner, Geoffrey and Kallaher, Ray and Manfra, Michael and Marcus, Charles and Higginbotham, Andrew P and Casparis, Lucas}, publisher = {Zenodo}, title = {{Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire}}, doi = {10.5281/ZENODO.4592435}, year = {2021}, } @inproceedings{13146, abstract = {A recent line of work has analyzed the theoretical properties of deep neural networks via the Neural Tangent Kernel (NTK). In particular, the smallest eigenvalue of the NTK has been related to the memorization capacity, the global convergence of gradient descent algorithms and the generalization of deep nets. However, existing results either provide bounds in the two-layer setting or assume that the spectrum of the NTK matrices is bounded away from 0 for multi-layer networks. In this paper, we provide tight bounds on the smallest eigenvalue of NTK matrices for deep ReLU nets, both in the limiting case of infinite widths and for finite widths. In the finite-width setting, the network architectures we consider are fairly general: we require the existence of a wide layer with roughly order of N neurons, N being the number of data samples; and the scaling of the remaining layer widths is arbitrary (up to logarithmic factors). To obtain our results, we analyze various quantities of independent interest: we give lower bounds on the smallest singular value of hidden feature matrices, and upper bounds on the Lipschitz constant of input-output feature maps.}, author = {Nguyen, Quynh and Mondelli, Marco and Montufar, Guido}, booktitle = {Proceedings of the 38th International Conference on Machine Learning}, isbn = {9781713845065}, issn = {2640-3498}, location = {Virtual}, pages = {8119--8129}, publisher = {ML Research Press}, title = {{Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks}}, volume = {139}, year = {2021}, } @inproceedings{13147, abstract = {We investigate fast and communication-efficient algorithms for the classic problem of minimizing a sum of strongly convex and smooth functions that are distributed among n different nodes, which can communicate using a limited number of bits. Most previous communication-efficient approaches for this problem are limited to first-order optimization, and therefore have \emph{linear} dependence on the condition number in their communication complexity. We show that this dependence is not inherent: communication-efficient methods can in fact have sublinear dependence on the condition number. For this, we design and analyze the first communication-efficient distributed variants of preconditioned gradient descent for Generalized Linear Models, and for Newton’s method. Our results rely on a new technique for quantizing both the preconditioner and the descent direction at each step of the algorithms, while controlling their convergence rate. We also validate our findings experimentally, showing faster convergence and reduced communication relative to previous methods.}, author = {Alimisis, Foivos and Davies, Peter and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 38th International Conference on Machine Learning}, isbn = {9781713845065}, issn = {2640-3498}, location = {Virtual}, pages = {196--206}, publisher = {ML Research Press}, title = {{Communication-efficient distributed optimization with quantized preconditioners}}, volume = {139}, year = {2021}, } @article{13356, abstract = {Self-assembly of nanoparticles can be mediated by polymers, but has so far led almost exclusively to nanoparticle aggregates that are amorphous. Here, we employed Coulombic interactions to generate a range of composite materials from mixtures of charged nanoparticles and oppositely charged polymers. The assembly behavior of these nanoparticle/polymer composites depends on their order of addition: polymers added to nanoparticles give rise to stable aggregates, but nanoparticles added to polymers disassemble the initially formed aggregates. The amorphous aggregates were transformed into crystalline ones by transiently increasing the ionic strength of the solution. The morphology of the resulting crystals depended on the length of the polymer: short polymer chains mediated the self-assembly of nanoparticles into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer assemblies, within which the crystalline order of nanoparticles was retained.}, author = {Bian, Tong and Klajn, Rafal}, issn = {1749-6632}, journal = {Annals of the New York Academy of Sciences}, keywords = {History and Philosophy of Science, General Biochemistry, Genetics and Molecular Biology, General Neuroscience}, number = {1}, pages = {191--201}, publisher = {Wiley}, title = {{Morphology control in crystalline nanoparticle–polymer aggregates}}, doi = {10.1111/nyas.14674}, volume = {1505}, year = {2021}, } @article{21081, abstract = {Macrocyclic peptides are an important class of bioactive substances. When inserting an aromatic foldamer segment in a macrocyclic peptide, the strong folding propensity of the former may influence the conformation and alter the properties of the latter. Such an insertion is relevant because some foldamer–peptide hybrids have recently been shown to be tolerated by the ribosome, prior to forming macrocycles, and can thus be produced using an in vitro translation system. We have investigated the interplay of peptide and foldamer conformations in such hybrid macrocycles. We show that foldamer helical folding always prevails and stands as a viable means to stretch, i.e. unfold, peptides in a solvent dependent manner. Conversely, the peptide systematically has a reciprocal influence and gives rise to strong foldamer helix handedness bias as well as foldamer helix stabilisation. The hybrid macrocycles also show resistance towards proteolytic degradation.}, author = {Dengler, Sebastian and Mandal, Pradeep K and Allmendinger, Lars and Douat, Céline and Huc, Ivan}, issn = {2041-6539}, journal = {Chemical Science}, number = {33}, pages = {11004--11012}, publisher = {Royal Society of Chemistry}, title = {{Conformational interplay in hybrid peptide–helical aromatic foldamer macrocycles}}, doi = {10.1039/d1sc03640h}, volume = {12}, year = {2021}, } @article{21082, abstract = {A novel chiral aromatic δ-amino acid building block was shown to fully induce handedness in quinoline oligoamide foldamers with the possibility of further increasing the bias by combining multiples of these units in the same sequence. Through its incorporation within the helix, both N- and C-termini are still accessible for further functionalisation.}, author = {Bindl, Daniel and Heinemann, Elisabeth and Mandal, Pradeep K and Huc, Ivan}, issn = {1364-548X}, journal = {Chemical Communications}, number = {46}, pages = {5662--5665}, publisher = {Royal Society of Chemistry}, title = {{Quantitative helix handedness bias through a single H vs. CH3 stereochemical differentiation}}, doi = {10.1039/d1cc01452h}, volume = {57}, year = {2021}, } @article{21552, abstract = {We present full-Maxwell topology-optimization design of a single-piece multilayer metalens, about 10 wavelengths λ in thickness, which simultaneously focuses over a 60° angular range and a 23% spectral bandwidth without suffering chromatic or angular aberration, a “plan-achromat.” At all angles and frequencies, it achieves diffraction-limited focusing (Strehl ratio >0.8) and an absolute focusing efficiency of >50%. Both 2D and 3D axisymmetric designs are presented, optimized over ∼105 degrees of freedom. We also demonstrate shortening the lens-to-sensor distance while producing the same image as for a longer “virtual” focal length and maintaining plan-achromaticity. These proof-of-concept designs demonstrate the ultra-compact multifunctionality that can be achieved by exploiting the full wave physics of subwavelength designs and motivate future work on design and fabrication of multilayer metaoptics.}, author = {Lin, Zin and Roques-Carmes, Charles and Christiansen, Rasmus E. and Soljačić, Marin and Johnson, Steven G.}, issn = {1077-3118}, journal = {Applied Physics Letters}, number = {4}, publisher = {AIP Publishing}, title = {{Computational inverse design for ultra-compact single-piece metalenses free of chromatic and angular aberration}}, doi = {10.1063/5.0035419}, volume = {118}, year = {2021}, } @article{21559, abstract = {Being a general wave phenomenon, bound states in the continuum (BICs) appear in acoustic, hydrodynamic, and photonic systems of various dimensionalities. Here, we report the first experimental observation of an accidental electromagnetic BIC in a one-dimensional periodic chain of coaxial ceramic disks. We show that the accidental BIC manifests itself as a narrow peak in the transmission spectra of the chain placed between two loop antennas. We demonstrate a linear growth of the radiative quality factor of the BICs with the number of disks that is well described with the developed tight-binding model. We estimate the number of disks when the radiation losses become negligible in comparison to material absorption and, therefore, the chain can be considered as practically infinite. The presented analysis is supported by near-field measurements of the BIC profile. The obtained results provide useful guidelines for practical implementations of structures with BICs opening up horizons for the development of radio-frequency and optical metadevices.}, author = {Sidorenko, M.S. and Sergaeva, O.N. and Sadrieva, Z.F. and Roques-Carmes, Charles and Muraev, P.S. and Maksimov, D.N. and Bogdanov, A.A.}, issn = {2331-7019}, journal = {Physical Review Applied}, number = {3}, publisher = {American Physical Society }, title = {{Observation of an accidental bound state in the continuum in a chain of dielectric disks}}, doi = {10.1103/physrevapplied.15.034041}, volume = {15}, year = {2021}, }